Human Settlement History of Papua New Guinea Highland Populations

Mian Li et al.

New Guinea was first settled at least 40,000 years ago and is currently home to ~11,000,000 people speaking nearly 1/6th of the world’s languages. The Eastern Highlands of New Guinea was unknown to the outside world until the 1930s. Highlanders lived extremely isolated lives, rarely venturing from their valley of birth because of rugged mountainous terrain and constant, low intensity warfare with their neighbors.

In order to gain insight into the effects of Pleistocene settlement and local isolation on the maintenance of genetic and linguistic diversity, we characterized the mtDNA HVSI diversity of 870 early contact Eastern and Southern Highlanders who donated their serum in the 1950s-1960s. These people were from 20 villages representing 14 languages. The majority of these villages are within a contiguous 75km diameter region of the Eastern Highlands. In addition, 200 whole mtDNA genomes, which distributed evenly across villages, were sequenced using the Illumina platform.

A total of 116 unique haplotypes were detected based on the mtDNA HVSI region and all were assigned to 4 haplogroups (P=54.9%,Q=43.8%, N13=1%,R14=0.3%) based on additional SNP data from the whole mtDNA data set. Preliminary analysis revealed a significant correlation (p<0.001) between genetic and linguistic distances, suggesting linguistic barriers have restricted gene flow. In addition, 25 heteroplasmic positions detected with Sanger sequencing were all confirmed with high-throughput Sequencing. Furthermore, the 200 New Guinea Highland whole mtDNA sequences we generated allowed us to refine the phylogeny of haplogroups P and Q and better understand the Pleistocene settlement of Sunda and Sahul.

MtDNA analysis reveals presence of ancestral lineages between coastal and highland populations in Papua New Guinea

Kate L. Derosa et al.

Nearly 1/6th of the world’s languages are spoken in New Guinea, reflecting its Pleistocene settlement and rugged mountainous interior. Archaeological evidence indicates trade of obsidian and shells, suggesting contact between the highland and coastal populations and thus potential gene flow between them.

We generated mtDNA HVSI sequences from 1,000 samples from early contact highlanders in 17 villages (n=50 each) representing 14 languages of the Trans-New Guinea Language Phylum. These data were then compared to those from eight coastal East Sepik Province populations to assess levels of gene flow between the two regions.

Preliminary analysis reveals the presence of shared mtDNA lineages between the eastern and southern highland and coastal populations. There is at least one lineage ancestral to all three geographic regions, determined by ≥50% of all populations within the geographic regions containing the same motif. Migration appears to be most prevalent between the southern highlands and the coast, as there are eight lineages within both regions ≥25%. Coalescent analysis of age supports the presence of ancestral lineages as the exclusion of the shared lineages increases age significantly for all groups except for the highland P haplogroup. This suggests the networks for all haplogroups, aside from highland P, become more dispersed and less related upon shared lineage exclusion, indicating the shared lineages are ancestral in nature. Thus trade routes between coastal and highland populations of New Guinea potentially provide routes for gene flow observed between highland and coastal populations.

Evidence of Coastal New Guinea Population Geneflow and Implications for the Southern and East Asian Migration Route Hypotheses

Ragsdale & Marsh

Genomic analyses of coastal New Guinea populations indicate both the Southern and Out of East Asia migration routes are important to the island’s settlement and recent geneflow. The mtDNA lineages found in individuals living in the Bismarck and Admiralty archipelagos are not typically observed on mainland New Guinea, suggesting a distinct ancestry originating in Southeast Asia. Evidence exists supporting both migration hypotheses, such as the division and expansion of Austronesian and non-Austronesian languages, the Lapita culture movement, and Denisovan ancestry placing New Guinea at an essential location for understanding human migrations across Oceania. 288 Southeast Asian and Melanesian mtDNA genomes collected from GenBank were used to compute genetic distances between populations and construct a neighbor-joining phylogenetic tree using MEGA version 7.0 freeware. The results exhibit close genetic affinities among mainland and archipelago New Guinea to the islands along the initial southern route including Java, Sulawesi, and Borneo, suggesting a common founding lineage. However, high differentiation is seen between the New Guinea mainland and archipelago populations, reflected in significant Fst values, indicating a potential secondary migration from East Asia, introducing new genetic variation into the eastern archipelago populations. As the proposed second migration traveled further from Southeast Asia and into Remote Oceania, genetic distances began to increase between these populations and mainland New Guinea, whereas distances have decreased between Remote Oceanians, specifically, the Solomons, Vanuatu, Fiji, and the New Guinea archipelagos, thereby further diversifying populations of mainland New Guinea from those of the Bismarck and Admiralty archipelagos.

Population genetics analysis of Southeast Asian Ovalocytosis in a cohort of individuals from Island Melanesia

Elizabeth A. Werren et al.

Malarial infection has been a major selective pressure on the human genome. This has led to the evolution of variable resistance mechanisms in humans, mainly in the form of hematologic disorders. A well-characterized malaria resistance allele found in individuals with Austronesian ancestry is a 27-bp deletion in the Band 3 protein-encoding gene SLC4A1. The deletion results in the formation of abnormal, oval-shaped erythrocytes, known as Southeast Asian Ovalocytosis (SAO). SAO erythrocytes confer protection against malaria by disrupting cytoadherence. However, potential frequency of the deletion is constrained by its lethal homozygous state. Previous evidence suggests SAO is under balancing selection in certain Austronesian populations. Island Melanesia is comprised of Austronesian and Papuan-speaking inhabitants whose ancestors independently migrated to the region ~5,500 and 50,000 years ago, respectively. We genotyped 452 Melanesian individuals with varying amounts of Austronesian ancestry to characterize the allele frequency distribution of the SAO deletion (24 from Lavongai, 195 from New Britain, 98 from New Ireland and 135 from Bougainville). The Austronesian population of Lavongai displayed the highest observed deletion frequency at 16.7%. We also observed the deletion in Papuan-speaking populations (Bougainville, New Britain, New Ireland) at a total frequency of 3.8%, indicating gene flow with surrounding Austronesian groups. To assess the role of selection in maintaining SAO among Island Melanesians, we DNA sequenced the exonic portions of SLC4A1. We applied standard population genetics tests to detect evidence of natural selection. Our results shed further light on the combined role of gene flow and natural selection in upholding SAO.

The Genomic History of the First Australians

Anna-Sapfo Malaspinas et al.

Reconstructing the population history of Aboriginal Australia has in the past been limited to investigations of the fossil human record and, more recently, the analysis of mtDNA. Understanding the origins of the First Australians through the analysis of complete genomes holds the potential to provide important new insights into the initial dispersal of Homo sapiens from Africa, but also for our understanding of the development of further population structure in ancient Australia. We have generated high-coverage genomes for 83 Aboriginal Australians and 25 Papuans from the New Guinea Highlands and identified a) Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations b) Papuan and Aboriginal Australian ancestors diversified 25–40kya, suggesting pre-Holocene population structure in the ancient continent of Sahul, c) Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya and d) population expansion occurred in northeast Australia during the Holocene. The results of our research provide a new population history for Ancient Australia.

The affinities of Homo floresiensis based on phylogenetic analyses of cranial, dental and postcranial characters

Debbie Argue et al.

Although Homo floresiensis has been known for 13 years, its phylogenetic status remains highly contentious. Bones that have been placed in the Homo floresiensis hypodigm have been interpreted in three ways: that the species is descended from an early hominin lineage; that it is a dwarfed descendant of Homo erectus; that the remains are those of anatomically modern humans that had genetic or metabolic disorders.

Here we present the results of parsimony and Bayesian phylogenetic analyses of an expanded morphological dataset comprising a comprehensive range of specimens for Australopithecus and Homo: Australopithecus afarensis, Australopithecus africanus, Australopithecus sediba, Homo habilis, Homo georgicus, Homo naledi, Homo ergaster, Homo erectus (Sangiran and Trinil), and Homo sapiens. We broaden the range of traits previously applied to the H. floresiensis question by including characters from the crania, mandibles, dentition and postcrania. This has not been attempted before and provides an unparalleled database to apply to the problem of the phylogenetic position of this species.

The new data and analyses support the hypothesis that H. floresiensis is an early Homo lineage and suggest that H. floresiensis is a long-surviving relict of an early (>1.9Ma) hominin. A close phylogenetic relationship between H. floresiensis and H. erectus or H. sapiens can be rejected – we conclude that H. floresiensis is not derived from either of these species. These results indicate a hitherto unknown hominin migration out of Africa.

Can Small be All? The Limited Commonalities of Mata Menge and Liang Bua Hominins on Flores

Maciej Henneberg et al.

The original diagnosis of Homo floresiensis from the Liang Bua skeletal remains listed among numerous others these defining elements: Small-bodied; endocranial volume similar to, or smaller than, Australopithecus africanus; lacks masticatory adaptations present in Australopithecus and Paranthropus; first and second molar teeth of similar size; mandibular coronoid process higher than condyle; mandible without chin. We already have shown in 2015 that these and many additional defining elements largely are those of the LB1 individual, since most LB specimens are represented by only one or two bones each. Even some of the few duplicated elements differ: The LB6 mandibular ramus is shorter than that of LB1 and lacks a coronoid higher than condyloid process. Statures originally were underestimated and are matched in regional extant small bodied humans, as are small, chinless mandibles. The Mata Menge (0.7 Ma) gnathic specimens include a fragment of mandibular corpus (SOA-MM 4) plus six teeth. These establish little other than small size within the already known human range. For example, SOA-MM1 shows uncorrected dimensions of 9.7 mm MD x 8.9 mm BL, close to Klasies River Mouth KRM14624 (9.3×8.8) and KRM43110 (10.2×9.1). Given the extremely limited Flores skeletal evidence, and the known unreliable correlations of body and brain size with tooth sizes, it is premature to suggest that the Mata Menge gnathic fragments establish any more than previously known archaeological evidence: the existence of hominins of as yet indeterminable taxonomic status on an island where Homo sapiens is known to have a living and archeological presence.

Human bones excavated at Liang Bua, Flores, Indonesia, were assigned to the new taxon “Homo floresiensis” although coexisting with Homo sapiens populations elsewhere. LB1 features (very low endocranial volume, short femora, flaring ilia, etc.) emphasized as diagnostic of a new hominin species are accompanied by other anomalous signs not noted initially, including craniofacial and other asymmetries. Contrasting explanations of brain and body sizes and proportions in LB1 overlook the significance of smaller-scale traits commonly referred to by clinical morphologists as minor physical anomalies (MPAs). Hospital surveys conducted by Merks and colleagues in the Netherlands scored patients for traits in 29 major anatomical areas subdivided into 98 smaller regions including a total of 683 single anomalies. In adapting the traits surveyed to LB1 limited skeletal remains we compared only subsets (74 traits) that pertained to the head: Neurocranium size (2 traits), shape (6), sutures (6), face (20), upper jaw (7), lower jaw (5), palate (10), teeth (18). After eliminating small endocranial volume and other disputed features, LB1 exhibited 7 MPAs, including brachycephaly, plagiocephaly, palate form, plus asymmetries in the face, upper jaw, lower jaw, and teeth. Most clinical MPA studies do not record occurrence over the threshold of ≥3 traits indicating an elevated likelihood of major malformation, but one showed that 36.7% of mentally retarded children had ≥5 MPAs while no control had ≥5. Above-threshold MPA trait occurrence in the greatly restricted subset scored for LB1 remains completely consistent with Down syndrome and independently signals developmental abnormality regardless of specific diagnosis.

Shifts in the distribution of rat body sizes through time at Liang Bua: New paleoecological insights into the extinction of Homo floresiensis and other endemic taxa

Elizabeth Grace Veatch et al.

Liang Bua, a cave site on the Indonesian island of Flores, is best known as the type locality of the enigmatic hominin species, Homo floresiensis. Excavations at Liang Bua have recovered large numbers of vertebrate skeletal remains, including over 230,000 skeletal elements that belong to at least five genera of murine rodents (i.e., rats). These taxa vary considerably in body mass from ~72 g to ~1,500 g. Temporal variations in the abundances of these differently-sized rats at Liang Bua could reflect important shifts in past climate, environment, and/or ecology over the past 190 thousand years (ka). To explore potential temporal variation in rat abundance during this time, we measured rat femora (N=10,212), humeri (N=1,474), and calcanei (N=372) from all currently recognized stratigraphic units at Liang Bua. A comparative sample of extant Southeast Asian murid species was used to estimate five body size classes for the subfossil murines at Liang Bua. Changes in the abundances of these body size classes across successive stratigraphic units were quantified using chord distance, and further explored using cluster and correspondence analyses. Results show a major shift in the distribution of rat body sizes at Liang Bua immediately following a volcanic eruption that occurred ~60 ka, suggesting that environmental change was part of the processes that ultimately led to the extinction of H. floresiensis and other endemic taxa ~50 ka ago. These results further underscore the importance of small mammal assemblages for interpreting the paleoenvironment and paleoecology of hominin sites.

Pelvic remains from the type specimen of Homo floresiensis (LB1/7) may be informative about the evolutionary affinities and locomotor repertoire of this enigmatic hominin, but have yet to be analyzed morphometrically. Here, we analyze the preserved anatomy using 3D geometric morphometrics and attempt a series of digital reconstructions of a full os coxa.

We collected a 3D landmark dataset from a sample of modern humans and fossil hominins tailored to the partial left os coxa of LB1, which lacks portions of the iliac crest and pubis. Principal components analysis indicated that modern humans are differentiated from early australopiths (Australopithecus afarensis, A. africanus) along the primary axis of shape variation, with H. floresiensis approximately equidistant to these two groups. H. floresiensis was more distinct from two large-bodied early Homo specimens along this axis, as well as from the Kebara Neanderthal and A. sediba, which were overlap the H. sapiens range. This component captured variation in ischial tuberosity shape and iliac blade flare.

To reconstruct the missing portions of the ilium and pubis, complete os coxae of A. afarensis (AL 288-1), A. sediba (MH2) and a small-bodied H. sapiens were warped to the shape of LB1 based on the regions of morphological overlap. Additional landmarks from the iliac crest and pubis resulted in better separation between modern humans and the full fossil sample. The two australopith-based reconstructions grouped together despite the different morphology of A. sediba and A. afarensis, while the human-based reconstruction fell at the periphery of the modern human range.

Face in the Sand: Island Rules, Biogeography, and the Fallacy of Palauan Hobbits

Stone & Fitzpatrick

The “Island Rule” is an ecogeographical principle which states that members of a given species will change body size based on either the (un)availability (dwarfism) or abundance (gigantism) of resources in the surrounding environment. While there are many examples of insular dwarfing and gigantism among various reptile, bird, and mammal species across different island regions, some controversy remains regarding the applicability of this phenomenon globally. One of the more recent and contentious cases regarding insular dwarfism in anthropology involves purported small-bodied humans from the Ucheliungs Cave in Palau, Micronesia that called into question the validity of Homo floresiensis as a separate species. While these results have previously been disputed based on a host of archaeological, biological, and linguistic data, we now present results from further test excavations conducted at Ucheliungs in 2015. In contrast to previously reported findings, our results indicate an abundance of faunal material, human remains, and artifacts at the site that call into question the methods and analyses used to document the presence of smaller individuals here. Along with new radiocarbon dates from the site, results instead support long-term use of the cave for both mortuary activity and possibly small scale marine foraging that is contemporary with the earliest known human activity in Palau. Results also support the need to carefully examine all aspects of archaeological and other lines of evidence to satisfactorily support a hypothesis suggesting the presence of insular dwarfing and challenge the assumption that small islands are marginal environments for prehistoric human populations.

Paleogenomic investigations of human remains from Rapa Nui

Fehren-Schmitz et al.

Since Easter Sunday of 1722, when Jacob Roggeveen became the first western seafarer to reach Rapa Nui, this remote island in the Eastern Pacific has inspired fiction and science regarding the origin and life of its inhabitants. While the Polynesian ancestry of the first settlers is widely accepted, other events in the population history of the people of Rapa Nui, especially contact with South America, remain controversial. Although researchers recently found signals of Native American admixture when analyzing modern ancestors of indigenous inhabitants of Rapa Nui – suggesting genetic contributions from South America prior to the European contact – there is still considerable doubt regarding the timing of that admixture event, or the directionality and origin of the trans-Pacific contact. Here we present the results of our paleogenomic investigations of seven samples excavated from Ahu Nau Nau, Anakena, by the Kon-Tiki Museum, dating to periods of pre- and post-European contact. Despite the challenging preservation and small material quantity of these rib samples, we were able to obtain complete mitochondrial genomes and low coverage genome-wide sequence data from four samples using a combination of shotgun sequencing and a novel whole genome enrichment assay. We combine the data with ancient and contemporary Native American, Oceanian, and global population data to find that the analyzed individuals fall well into the genetic diversity of Polynesian populations. We find no admixture with Europeans in the post-contact samples with an increased Melanesian component, while an admixture with Native Americans remains inconclusive.

The effect of mobility and modernization on co-residence patterns in Batek hunter-gatherers: a longitudinal analysis

Kraft et al.

Group living is a hallmark feature of many social species, including humans. Recent evidence in hunter-gatherers of a high degree of unrelatedness among co-residents has led some researchers to conclude that humans exhibit a unique co-residence structure. But previous studies present a static picture of hunter-gatherer co-residence, and therefore cannot speak to the ecological factors that influence variation in patterns of group living. Here we present the co-residence structure of Batek hunter-gatherers in Peninsular Malaysia, using longitudinal data collected between 1975 and 2016. We use these data to ask how reduced mobility and modernization (e.g. increased access to agricultural food products) have affected Batek co-residence patterns over time. We find that in the mid-1970’s, the co-residence structure of mobile Batek bands closely resembled published results for other hunting and gathering populations. We also found that Batek co-residence patterns changed through time, resulting in overall decreases in within-camp relatedness as group size and the degree of settlement increased. However, these effects were mitigated in part by the spatial modularization of relatedness within camps, driven by the formation of clusters of primary kin. Our results demonstrate that hunter-gatherer co-residence is flexible and can be quickly adapted to modern conditions, and raise fundamental questions about how hunter-gatherer individuals choose who they want to live with and the dynamic process by which group membership is determined.

Defining Homo or identifying Homo? The role of the genus in hominin taxonomy

BRIAN A. VILLMOARE.

The role of the genus in hominin taxonomy has been highlighted recently by discoveries proposed to be early member of Homo (e.g. Berger et al., 2010, Villmoare et al., 2015). Wood and Collard (1999) and Collard and Wood (2007, 2015) proposed that a genus should be a monophyletic group, but only one ‘whose members occupy a single adaptive zone’; this would mean removing the earliest specimens now attributed to Homo, as they have been inferred not to share the adaptive zone of Homo erectus and later species in the genus. Schwartz and Tattersall (2015) agree, and propose using a finite pattern of variation to ‘define’ the genus, arguing that the present use of the genus Homo is overly broad and not in line with broader taxonomic practice.

I examine this hypothesis by contrasting hominin systematic practice with current taxonomies across evolutionary biology, including vertebrates, invertebrate animals, and plants. One clear conclusion is that, with few exceptions, across evolutionary biology, genera are consistently monophyletic, with no attempt to parse more primitive members out. Similarly, there is no specific template of morphological or behavioral diversity. Genera can range from one to more than a thousand, and many genera are remarkably diverse. Because of this, any attempt to ‘define’ the genus Homo is suspect, as modern taxonomic practice requires only synapomorphies for identification of clades at any level, and there is no justification for identifying levels of variation that a genus may not exceed.

Dead end evolutionary lineage, says the White man: the evolution of Homo erectus and Homo sapiens in Asia

SHEELA G. ATHREYA.

The role of Asian populations in models of Middle and Late Pleistocene hominin evolution has historically been framed in two ways. Before 1948, the predominant view was that East/Southeast Asian Homo erectus was a “prehominid” species ancestral to Homo sapiens. After 1948 with the publication of Movius’s monograph, Asia was treated as a “marginal region of cultural retardation” that played no role in the evolution of H. sapiens. The perpetuation of this perspective into the late 20th and early 21st century has had the effect of marginalizing the Asian data in global models of human evolution. Perhaps more importantly, the contributions of scholars from the region have been viewed with skepticism, thus effectively keeping their voices from contributing to an understanding of our evolutionary history. In keeping with the theme of the symposium, this presentation will discuss the implications of these events on two levels: first, in terms of how they impacted the developing narrative of human evolution; and second, in terms of how they reflect biases in the way Western physical anthropologists conduct scientific research. A proposal for opening the science of paleoanthropology to a broader regional and cultural range of scientific perspectives is offered.

Revising the hypodigm of Homo heidelbergensis, a view from the Eastern Mediterrannean

MIRJANA ROKSANDIC

The hominin mandible BH-1 from the Middle Pleistocene cave of Mala Balanica suggested a possibility that human populations in this part of the continent were not subject to the process of Neanderthalization observed in the west. Paleontological and paleoanthropological evidence from the Balkans is reviewed in the context of the Eastern Mediterranean geographic entity. Current hominin fossil record of the early Middle Pleistocene in the region suggest that Europe was inhabited by two different populations, a population in the west of the continent with developed derived Neanderthal morphology, and a more variable population in the east characterised by a combination of plesiomorphous and synapomorphous traits. In order to continue using the nomenclature of Homo heidelbergensis, the current hypodigm needs to be revised to include only the specimens from the latter group.

The diet of Homo antecessor

Marina Lozano et al.

The diet of the earliest inhabitants of Europe has been previously inferred from archaeological evidence. However, the effects of dietary preferences on teeth remain unknown. Here, we report a novel approach through quantitative analysis of buccal microwear on cheek teeth in well-documented Gran Dolina-TD6 Atapuerca (Burgos, Spain) hominins (≈0.8 million years ago), since microwear on non-working molar surfaces reflects the physical properties of chewed foodstuffs and long-term trends in dietary signals.

The lack of evidence in the use of fire in the TD6 level indicated that non-thermal hard and brittle raw foods increased the abrasiveness of the diet. In basis to this unique dental microwear pattern found, we suggest that Homo antecessor was specialized in the ingestion of fracture-resistant foodstuffs such as Underground Storage Organs (USOs) and scavenged or hunted gritty meat resources. This mechanically-demanding dietary regimen would have required strong bite force production. The microwear density reduction in Middle Pleistocene populations suggest differences in food mechanical properties linked to more advanced tool technologies.

Australopithecus sediba and the Origin of Homo: Questionable Evidence from the Cranium of the Juvenile Holotype MH 1

Kimbel & Rak

Malapa Hominid (MH) 1, an immature individual whose second permanent molars had recently reached occlusion at the time of death, is the holotype of Australopithecus sediba, a 2-myr-old South African taxon that has been hypothesized to link phylogenetically australopith-grade hominins to Homo. Given the existence of 2.8 myr-old fossils of the genus Homo in eastern Africa, this hypothesis implies a ghost lineage spanning at least 800 kyr. An alternative hypothesis posits a unique relationship between A. sediba and A. africanus, which predates the Malapa hominins in southern Africa and whose phylogenetic relationships remain ambiguous. The craniofacial morphology of MH 1 looms large in the framing of the two hypotheses, which we investigated in two ways. First, we investigated whether the craniofacial morphology of MH 1 was ontogenetically stable at death. Based on data from a late-growth series of chimpanzee, gorilla, and modern human crania, we found that key aspects of MH 1’s resemblance to Homo are accounted for by its immaturity. Second, we studied MH 1 with an eye to identifying craniofacial synapomorphies shared with A. africanus. In this case, MH 1 shows unambiguous affinities in its zygomaticomaxillary and supraorbital morphology to crania from Sterkfontein Member 4, which we found to exhibit unusual derived morphology compared to Homo and other australopiths. We argue that MH 1 provides clear evidence that A. sediba was uniquely related to A. africanus and that the hypothesis of an extensive ghost lineage connecting A. sediba to the root of the Homo clade is unwarranted.

The origin of our species: an ancestral morphotype for modern humans

Mounier & Lahr

The origin of H. sapiens is a major focus in palaeoanthropology; yet, many unanswered questions remain. The morphological variation of Late Middle Pleistocene (LMP) African hominins is largely unknown, thus precluding the definition of boundaries of variability in early H. sapiens, and the interpretation of individual specimens.

This study uses maximum likelihood and 3D geometric morphometrics within a Brownian model of evolution to predict possible morphologies of a virtual last common ancestor (vLCA) of modern humans from a simplified phylogeny: early Homo (N=2), Neandertals (N=4), early H. sapiens (N=2), Africans (N=5), Eurasians (N=2) and Oceanians (N=2). Each specimen is described by 797 semi-landmarks.

The vLCA is computed as a set of shape coordinates used to warp a modern skull to obtain a fully rendered 3-dimensional shape of the predicted ancestral morphology. We compare the vLCA to LMP African fossils (KNM-ES 11693, Florisbad, Jebel Irhoud, Omo II, and LH 18) by aligning and scaling them (GPA) with the vLCA, in order to project them in morphospace, and to quantify shape differences between them and the vLCA (color-coded deviation spectrum) under various anatomical configurations.

Our results identify the strongest similarities between the vLCA and KNM-ES 11693 and Florisbad. Additionally, they underline the wide range of morphologies exhibited by the LMP fossils, some of which present stronger similarities with Neandertals or early Homo than with the vLCA. Such diversity may be explained by a complex transition towards modern humans, with chronological overlap between individuals showing a mosaic of derived and archaic traits.

Modern Human Variation in Brain Size: Implications for the Dmanisi Hominins and other Fossil Taxa

Schoenemann & Holloway

How much variation in a particular biological characteristic one can expect within a species is an important consideration when trying to determine whether sets of fossil specimens could conceivably be members of the same species. Some have suggested that the range of morphological variation among the Dmanisi hominins indicates they are likely not members of the same species (e.g., Schwartz et al. 2014). In response, Zollikofer et al. (2014) argue the Dmanisi hominins are not too variable to preclude their being members of the same species. One character not specifically discussed by Zollikofer et al. (2014) is brain size. The Dmanisi hominins range from 546 cc to 775 cc (amounting to 35.5% of their mean cc). Is this unusually large with respect to known within-species ranges of variation? Data on brain size variation within modern humans, from an MRI study of 36 same-sex female sibling pairs (72 individuals in total) shows that the largest within-family sib difference (234.9 cc) amounted to 20% of their mean cc. The largest between-individual (non-sib) difference amounted to 34.6% of the mean cc – very close to that found among the Dmanisi hominins. Given this sample only included females, and given the sex difference in brain size (~10%), these estimates can be considered lower bounds of the likely range of within-species variation in brain size within humans. Thus, the range of variation in cranial capacity seen among the Dmanisi hominins is not strong evidence that they are members of different species.

Craniofacial Variation in Middle Pleistocene Hominins

Suzanna White et al.

Middle Pleistocene hominins have been found across the Old World, and document a wide range of craniofacial morphology within a relatively small sample. These fossils are frequently classified as Homo heidelbergensis sensu lato (s.l.), yet some researchers believe that this grouping introduces more variation than should be expected in a single hominin species. This paper aims to investigate the taxonomic status of the Middle Pleistocene hominins, and address two hypotheses: that the craniofacial variation in Homo heidelbergensis s.l. is less than or equal to that found in a single, widespread Catarrhine species; and that any divisions within this group are not comparable to those found between Catarrhine subspecies.

A 3D geometric morphometric method is employed, involving the placement of landmarks and semilandmarks on and around the supraorbital torus, due to its high preservation and phylogenetic utility, both within Primates and Middle and Late Pleistocene hominins. The comparative sample consists of over 800 specimens from Homo, Pan, Gorilla, Papio and Macaca species and subspecies, as well as ten disputed Homo heidelbergensis s.l.. Results confirm both hypotheses: the variation in the supraorbital region of the Middle Pleistocene fossils is less than that of a widespread Catarrhine species; and this variation does not indicate the existence of any subgroups that may be representative of separate taxa within this species. These results support the single, monotypic species classification of Homo heidelbergensis s.l. and the use of multiple, appropriate models of intra- and intergroup variation when studying biological variation in extinct hominin groups.

The middle Pleistocene human pelvis: a comparison across Eurasia

Alejandro Bonmati et al.

A significant number of human pelvic remains have been published since the first fossil hip bone attributed to the genus Homo was discovered in the Neander Valley. However, there are still important gaps in the fossil record. Only three Eurasian middle Pleistocene remains are well enough preserved for comparative purposes: the virtually complete pelvis from Sima de los Huesos site in Spain (SH Pelvis 1), the quite complete hip bone from the Chinese cave of Jinniushan and the partially complete hip bone from the French cave of Arago (Arago 44). In the present study we make a direct comparison between Jinniushan and SH Pelvis 1 for the first time taking advantage of CT scans of the original fossils.

The overall morphology of SH Pelvis 1 and Jinniushan is very similar. These two specimens are both very large overall. They retain the pelvic breadth seen in earlier, smaller bodied humans. Most differences between them can be explained as the result of sexual dimorphism. In particular, we think that these two specimens can be attributed to a male (SH Pelvis 1) and female (Jinniushan) individual due to differences in pubic and sciatic notch morphology, however they closely match each other in size. The similarity in pelvic morphology that we see across the Eurasian continent suggests that middle Pleistocene hominins shared a broad pelvis similar to their lower and middle Pleistocene ancestors (e.g. KNMER 3228 and OH28) but scaled up to a larger body size.

“Rogue” Taxa and Hominin Phylogeny

Mana Dembo et al.

Obtaining a well-supported phylogenetic tree for the hominins is an important goal for palaeoanthropology. However, studies have often yielded trees that contain weakly supported relationships. In the study reported here, we investigated whether this is due to some hominins species being “rogue” taxa. Rogue taxa are species that move around in phylogenies and therefore decrease resolution and support levels. This phenomenon is caused by ambiguous or contradictory phylogenetic signal. The goals of the study were a) to identify any rogue taxa, and b) to assess their impact on the support for different nodes.

We began by running a dated Bayesian analysis using a supermatrix of 391 craniodental characters pertaining to 25 taxa from the last seven million years of hominin evolution. Using the resulting posterior distribution of trees we identified rogue taxa using the software RogueNaRok. The species identified as rogues were then removed iteratively in subsequent analyses. We conducted Bayesian analyses with the pruned taxon sets to assess the improvement of nodal support in the resulting phylogenies.

Seven fossil hominin taxa assumed varying and contradictory positions in the phylogenies and therefore were identified as rogue taxa by RogueNaRok. We found a dramatic improvement in nodal support with the removal of any of these taxa, but in particular with the removal of Kenyanthropus platyops, Homo naledi, and Homo floresiensis. A careful consideration of these rogue taxa and their characters may improve the overall accuracy and support for hominin phylogenies.

The rapid spread of Homo erectus from Africa, especially into the more temperate climates of Eurasia, has been variously attributed to technological, energetic, and foraging shifts. The temporal and regional anatomical variation in H. erectus suggests a high level of developmental plasticity, or the ability to modify development in response to environmental conditions. Developmental plasticity, a key factor in the ability of H. sapiens to occupy a variety of habitats worldwide, results in differences in size, shape, and dimorphism across populations. These differences predict regional variation, overall smaller adult sizes, and lower levels of dimorphism in instances of resource scarcity and high predator load. However, determining whether the human pattern of variability is unique and relatively great compared to other widely dispersed nonhuman primates, and whether it can be retrieved from the skeletal record of these taxa is a non-trivial question. As part of a broader study that looks at metric variation in 35 human and nonhuman primate ‘populations’ from known environmental contexts and 14 time- and space- restricted paleodemes of H. erectus and other fossil Homo, here we delve deeper into the relationship between somatic and skeletal variation in recent Homo sapiens and Macaca mulatta. We find that skeletal measurements track somatic measurements with varying accuracy across different types of variables but with similar patterns in both humans and macaques. Further, skeletal and somatometric variables yield similar patterns of sexual dimorphism within groups, suggesting that inferences about fleshed bodies may be made from carefully chosen skeletal proxies.

Human variability in the earlier Middle Pleistocene of Europe is poorly known, which makes it difficult to assess patterns of human diversity and possible regions for ancestral populations associated with the western Eurasian spread of the Acheulian technocomplex. A recently discovered partial cranium from the Gruta da Aroeira may shed some light on this period. U-series dating provides an age ˜400 ka, placing the fossil in the relevant time period . This cave site was first excavated between 1998 and 2002, revealing a rich collection of Acheulian bifaces in association with large mammals and two human teeth . Work resumed in 2013, intent on reaching bedrock and establishing the chronology of the sequence, which spans 4 m and comprises three major stratigraphic units. A partial human cranium encased in rock-grade breccia was discovered at Unit 2. It consists of a large part of the right side of a braincase, lacking the occipital bone, but also preserving a portion of the left side of the frontal squama and supraorbital torus, as well as the interorbital region, including the vertical part of the nasal bones. A fragment of the right maxilla, with two molars partially preserved, was also found attached to the calvarium but not in anatomical position. Some Aroeira features are primitive traits found on some Middle Pleistocene fossils from the Sima de los Huesos, Caune de l’Arago and Ceprano, but not found in Neandertals and are consistent with a geological age between 400 ka and 500 ka.

Recent studies have demonstrated the utility of the outline shapes of deciduous upper and lower second molars and the deciduous upper first molar for diagnosing taxa – especially Homo neanderthalensis and H. sapiens. Building on these, here we assess the taxonomic significance of the crown outline of the deciduous lower first molar (dm1) through principal components analysis and quadratic discriminant analysis. We test whether the crown shape of the dm1 separates H. neanderthalensis from H. sapiens, and explore whether it can be used to correctly assign individuals to taxa. Our recent human sample includes 103 individuals from Africa, Europe, South America, India, and Australia. Our comparative sample includes 3 early H. sapiens, 8 Upper Paleolithic H. sapiens and 13 H. neanderthalensis individuals. Our results indicate that H. neanderthalensis dm1s cluster fairly tightly and separate well from those of Upper Paleolithic H. sapiens. However, the range of shapes in the recent human sample overlaps ranges of all fossil samples. Consequently, results of the quadratic discriminant analysis based on the first five PCs representing more than 90% of the variation were mixed. Lower dm­­1­­s were correctly classified in only 77.2% of the individuals: H. sapiens had better success (78.1%) than H. neanderthalensis (69.2%). When the analysis was re-run without recent humans (for whom variation was extensive) accuracy improved: 92.3% of H. neanderthalensis and 87.5% of Upper Paleolithic H. sapiens were classified correctly. We conclude that crown shape of dm­­1 is useful for identifying H. neanderthalensis and H. sapiens during the late Pleistocene.

Modern humans may have first encountered and interbred with Neanderthals during their dispersal out of Africa. This interbreeding event could have occurred in either the Levant or southern Arabia depending on whether modern humans took a more northern or southern route. We test Levantine and southern Arabian populations to see if they bear the same Neanderthal haplotypes as a way of determining where modern humans first interbred with Neanderthals.

In our analyses, we generated data on 607,938 autosomal SNPs in 90 Yemeni individuals using the Affymetrix Human Origins array. We also collected previously published data from Levantine and other southern Arabian populations, other comparative populations from around the world, and Neanderthal and Denisovan genome sequences. Using this extensive dataset, we identified 1802 Neanderthal SNPs found in previously identified introgressed haplotypes and compared their frequencies in Levantine and southern Arabian populations.

When analyzing all SNPs, Levantine and southern Arabian populations have similar levels of overall Neanderthal ancestry. When we focus on the Neanderthal SNPs identified in introgressed haplotypes, we find that a small percentage of SNPs (~10%) have significantly different frequencies between the Levant and southern Arabia, but the majority of SNPs have similar frequencies in both regions. We speculate that the Neanderthal ancestry in Levantine and southern Arabian populations may originate from the same pulse(s) of Neanderthal introgression.

Diverse Patterns of Neanderthal Introgression in Western Asia

RECEP O. TASKENT et al.

Neanderthals contributed genetic material to the ancestors of present-day Eurasians via multiple introgression events. The initial introgression event most likely occurred in Western Asia during the out-of-Africa migrations of modern humans. Our earlier analyses suggest that Western Eurasian populations show highly variable patterns of Neanderthal introgression in their genomes. We hypothesize that this variation could be related to more recent, population-specific migrations. Indeed, it has previously been shown that Western Asian populations show significant genetic structure, essentially creating a quilt pattern, which contrast with the clinal patterns of genetic variation observed in Europe. To investigate whether such genetic structure can explain different levels of Neanderthal introgression among Western Asian populations, we conducted S* statistics based analyses of dozens of genomes and identified the haplotypes introgressed from Neanderthals. We then specifically analyzed introgression patterns in Turkish genomes as compared to those in other Eurasian genomes. Our results revealed distinct introgressed haplotypes that show more than expected population differentiation between Turkish genomes and those of other Eurasian populations. Furthermore, we identified introgressed haplotypes in the Turkish population, which are absent in other European populations. Based on further population genetics analyses, we argue that complicated population histories of Western Asian populations along with a population-specific adaptive forces are likely responsible for the complex Neanderthal introgression patterns observed across Western Asia.

Simultaneous Estimates of Archaic Admixture and Ancient Population Sizes

Rogers and Bohlender

To estimate archaic admixture, one must control for the sizes and separation times of ancient populations. We describe a new method that provides simultaneous estimates of these parameters in complex models of population history. Preliminary results indicate that (1) throughout Eurasia, the level of Neanderthal admixture is uniform (about 2%) and Denisovan admixture is near zero; (2) contrary to published results, there is no evidence of excess Neanderthal DNA in East Asia; (3) the situation is different in Melanesia, which exhibits higher levels of admixture from both archaic populations, (4) the population ancestral to modern humans numbered about 18,000 as did that ancestral to moderns and archaics; and (5) the population ancestral to Neanderthals and Denisovans may have numbered only a few dozen individuals.

It’s all in the wrist: New Neandertal carpal bones from El Sidrón (Asturias, Spain)

Tracy L . Kivell et al.

Twenty-eight adult carpal bones of Homo neanderthalensis, representing all elements of the wrist, have been uncovered from the site of El Sidrón (Asturias, Spain) between 1994-2010 and dating to 49,000 years old. Within this sample, several carpal bones can be associated to the same individual with reasonable certainty to make up a complete right carpus. Here we provide a qualitative and quantitative comparative morphological description of these carpal bones, focusing on the scaphoid (n=6), trapezium (n=2), capitate (n=5) and hamate (n=2). The morphology is discussed within the context of other European and Near Eastern Neandertals, early and recent H. sapiens, and other fossil hominins, including australopiths and H. naledi. Overall, the carpal morphology of the El Sidrón sample shows many of the typical characteristics that distinguish Neandertals from H. sapiens, including a relatively flat, broad trapezium-first metacarpal articulation and a more radially-oriented capitate-second metacarpal facet. However, there are several features of El Sidrón carpal bones that distinguish them from other Neandertals; the tubercle of the trapezium is small with limited projection, while the scaphoid tubercle and hamate hamulus are among the largest compared with all known Neandertals. Furthermore, of the six scaphoids found, half show a fused but distinct “os-centrale portion”, while another is a bipartite scaphoid. This high frequency of developmental abnormalities offers support to previous evidence of a close genetic relationship among the 13 individuals found at El Sidrón.

The presence of Neanderthals in the Altai mountains of Siberia has been suggested since the 1980s, following the discovery of human remains associated with Middle Palaeolithic industries at Okladnikov and Denisova caves. These remains had few morphologically diagnostic traits, but analyses of mitochondrial and nuclear DNA supported the assignment of some of these fossils to Neanderthals, whereas others belong to another group, the Denisovans. R

Since 2008, our team has been excavating Chagyrskaya cave in the Charysh river valley, about 100 km west of Denisova. The site preserves about 2 m of Pleistocene deposits, which date to the transition between OIS 4 and 3 based on 14C dates and environmental data. The excavations yielded more than 100,000 lithics and about 150,000 animal bones, as well as 75 hominin fragments.

In this presentation we will focus on the dental remains, which consist of 20 isolated teeth and 7 teeth in mandible and maxilla fragments. The assemblage derives from at least two children and three adults, and it shows a large number of Neanderthal traits in the dentition. These include midtrigonid crests on the lower molars, large and projecting hypocones on the upper molars, asymmetrical lower fourth premolars and strongly shoveled upper incisors with a convex labial surface.

We will discuss the morphology of these specimens in a comparative context and their implications for our understanding of the easternmost Neanderthals.

One of the most abundant proteins in human saliva, mucin-7, is encoded by the MUC7 gene. In last year’s AAPA meetings, we presented the adaptive evolution of copy number variation of subexonic PTS-repeats within MUC7 among primates. Here, we present several lines of evidence suggesting that PTS-repeat copy number variation has evolved through at least 2 recurrent events in the human lineage, generating multiple haplotypic backgrounds carrying 5 or 6 PTS-repeat copy number alleles. Population genetics analyses suggest that one of the recurrent haplotypes carrying a 5 PTS-repeat copy is an unusually divergent sub-Saharan African lineage. Using simulation-based analyses, we now verified recent observations that an introgression event from an archaic African hominin best explains haplotypic variation in a small, but observable number of loci in sub-Saharan Africans. Then, we were able to cluster MUC7 with 93% confidence among loci where signatures of introgression were observed. Based on these, we conclude that some of the MUC7 haplotypic variation originated in an unknown African hominin population and introgressed into ancestors of modern Africans. In addition, resolving the haplotype structure of recurrent copy number variation of PTS-repeats, we were unable to confirm previous associations of 5 PTS-repeat copy alleles with protection against asthma in genome wide association studies. Instead, we revealed a significant association between MUC7 haplotypic variation and oropharyngeal microbial composition. To our knowledge, our study is the first example of archaic introgression in Africa involving copy number variation of coding sequences.

High Heritability and Ancestry Dominance are behind the Genetics of Short Stature in South African KhoeSan Populations

Meng Lin et al.

Adult height is one of the classic anthropometric traits studied in different human populations, with its genetic architecture extensively explored in Europeans. It is considered greatly polygenic and additive, with a high narrow sense of heritability (~ 80%) from early twin studies. To gain a better understanding of how genetic components affect stature variance in indigenous cohorts, we assayed statures in two KhoeSan communities, ≠Khomani San and Nama (n=400) in the rural Kalahari and Richtersveld Deserts of South Africa. These populations have continued possessing similar short statures (~155cm) compared to documented in 1940s (Trevor, 1947). Both our pedigree-based and genotyping inferred identity-by-descent (IBD) heritability estimates of height in the KhoeSan were excessively high (h2=0.95 and 0.89, respectively). Simultaneously a bottom-up estimate using pairwise relationships from SNP array and exome data closely matched the pedigree results. Despite a greater environmental and household homogeneity in these populations, we were able to observe small house household effect on height through higher IBD-based estimate in first-degree relatedness (h2=0.94). Considering recent admixture with Bantu-speakers and Europeans in the KhoeSan, we uncovered signals from certain ancestries contributing dominantly to stature variation through admixture mapping. The difference on ancestry heterozygosity between the two populations genetically agrees to the different documented timing of admixture with Bantu-speakers in the two communities. Taken together, these results show that the genetic architecture of height in KhoeSan endogamous cohorts are likely to differ from previously known in European populations.

Several genes that are responsible for the lighter skin color in Europeans as compared to Africans has been discovered, but our knowledge of global skin color remains incomplete without the identification of the primary polymorphisms responsible for the lighter skin of East Asians and/or Amerindians. To map those polymorphisms, we searched for populations admixed for either East Asian or Amerindian ancestry and a darker-skinned ancestry. The Orang Asli of Malaysia and the Kalinago of Dominica are the only two populations we found with such an admixture that also lacked significant European admixture that would otherwise confound our analysis. Both groups exhibit large variation in skin pigmentation. DNA samples and skin reflectance measurements were collected from a total of >1000 individuals. Skin pigmentation, expressed as Melanin Index, ranged from 20 to 80 units, averaging 47.6 and 45.8 for the Orang Asli and Kalinago, respectively. We excluded samples with either of the most common European skin color alleles, SLC24A5A111T and SLC45A2L374F from our downstream analysis. Admixture analysis of the Kalinago subsample showed 61% Amerindian, 31% African and 8% European ancestry, representing the highest Amerindian ancestry known among Caribbean populations. Albinism in the Kalinago was found by exome sequencing of an albino and an obligate carrier to be caused by a 4bp inversion in OCA2. Orang Asli genotyping revealed that the Negritos are distinct, and that the six Senoi subtribes show significant diversity and that a highland Senoi subtribe is distinct from the rest of the Senoi.

A Complex, Polygenic Architecture for Lightened Skin Pigmentation in the Southern African KhoeSan

Alicia R. Martin et al.

While >200 genes have been associated with pigmentation in animal models, fewer than 15 have been directly associated with skin pigmentation in humans. This has led to its characterization as a relatively simple quantitative trait. We show that skin color is more variable in admixed and equatorial populations by comparing phenotypes from ~5000 individuals in >30 populations, providing evidence of increased polygenicity closer to the equator. Strikingly, no quantitative gene discovery efforts for pigmentation have yet been published in continental Africa, despite skin pigmentation varying more there than any other continent. Light skin pigmentation is observed in the southern latitudes of Africa among KhoeSan hunter-gatherers of the Kalahari Desert. The KhoeSan are unique in their early divergence from other populations, dating back at least ~100,000 years. We demonstrate that skin pigmentation is highly heritable (h2>0.85), with similar estimates from pedigrees identified via ethnographic interviews, unrelated population-based samples, and haplotype sharing. Further, genes previously associated with skin pigmentation, rapidly evolving genes, and pigmentation genes discovered in animal models explain significantly more heritability than random genes. We show that some canonical pigmentation loci, including SLC24A5, are polymorphic in the KhoeSan and at higher frequency than explained by recent European admixture alone. We identify novel skin pigmentation loci, including near SMARCA2 and TYRP1, using a genome-wide association approach complemented by targeted resequencing in >440 individuals. Our results suggest that pigmentation loci can evolve rapidly in response to latitude and highlight the utility of studying geographically and genetically diverged populations for understanding human adaptation.

Omo-Kibish pelvic morphology and implications for body form in the earliest modern humans

Ashley S. Hammond et al.

The Omo-Kibish skeleton (Omo I) is the earliest known anatomically modern human (~195ka). Much of what we thought we knew about Omo I stems from the cranium, which was assumed to be a male primarily because of its large size, but a more recently-recovered os coxa from the same site has been preliminarily described as displaying female-like morphologies. If early modern human females were as large as Omo I, this could have important implications for the paleobiology of early modern humans.

Here we re-evaluate the sex of the Omo I hipbone based on indicators such as sciatic notch shape, preauricular sulcus form, and piriform tubercle morphology. We assess pelvic breadth by digitally re-aligning the ilium along the edge of a well-preserved step fracture. Finally, we predict stature from hip joint dimensions using published regression formulae.

The pelvic morphology of Omo I is consistent with a female sex attribution. The acetabulum size is large, even exceeding the size of many Neanderthals, resulting in stature estimates that are relatively tall for a female (172‐184 cm). When the ilium is repositioned into a normal contour, pelvic breadth is consistent with that of lower latitude modern human populations. Our findings suggest that earliest modern humans were tall, and retained fairly robust postcrania like earlier Pleistocene hominins. Since breadth and size of the pelvis are associated with thermoregulatory adaptations, Omo I is key for understanding the pelvic morphology of the earliest modern humans prior to human global expansion, regional adaptation, and admixture.

A Study of Structural Variants in Ancient Genomes and their Introgression into Modern Humans

Skyler Resendez et al.

Structural variants, which are variations of the copy number, location or orientation of segments of DNA rather than single nucleotide differences, have recently been shown to play major roles in recent human evolution. However, to our knowledge, no previous study directly evaluated the landscape of structural variants in ancient genomes. Here, we used available bioinformatics tools to discover structural variants in the genomes of the Altai Neanderthal, Denisovan, and a 45 thousand year old anatomically modern human. Our data provide a snapshot of hominin genomic variation in ancient Central Asia (Siberia) between 40-55 thousand years ago. For comparative purposes, we also sequenced a modern European genome at similar read-depth to the ancient genomes (~30X) and conducted the same structural variation discovery analysis. Overall, we found that each ancient genome had between 5,032-8,757 duplications and 3,212-3,900 deletions. In contrast, we found 1,508 duplications and 8,435 deletions in the modern European genome. Furthermore, we documented significant differences in the average size and exonic content among ancient genomes. We conducted several downstream analyses to investigate the technical, demographic and adaptive reasons underlying the disparity between structural variation distribution in ancient and modern genomes, as well as between different hominin species. In addition, we resolved the haplotype structure of a complete gene deletion (SPATA45), which likely introgressed from Neanderthals into the modern human lineage.

Khoe-San and the origins of modern human cranial diversity

Philipp Gunz et al.

A number of fossils from North, South, and East Africa document the early stages of our species, and fossils from the Levant document the presumed first wave of migration out of Africa. However, large gaps in the fossil record make it difficult interpreting the evolutionary processes and population dynamics shaping the cranial diversity of modern humans.

Here we use 3D geometric morphometrics based on landmarks and semilandmarks to compare cranial shape in a worldwide sample of recent and fossil humans from Africa, Europe, and Asia (N=256). Given that many Homo sapiens fossils are larger than recent Homo sapiens, we use multivariate regressions of cranial shape on cranial size to quantify static allometry and visualize how evolutionary changes of cranial size within the modern human lineage affect cranial shape.

We show that in a principal component analysis of shape Upper Paleolithic Homo sapiens fossils fall close to the center of all recent modern humans. Notably, Khoe-San also cluster near the center of recent Homo sapiens and are close in shape to Upper Paleolithic fossils and Qafzeh 9.The present-day Khoe-San therefore retain many aspects of the ancestral Homo sapiens cranial morphology, however much less pronounced owing to a gracilization of cranial features that occurred before the Holocene. Our results reconcile cranial morphology with recent genetic studies, which have identified deep genetic roots of the Khoe-San.